Below is a list of specialised set of microbial genomics-focussed analysis and visualisation tools that will be integrated into the Galaxy platform under this project. These will provide the initial functionality required for primary/secondary analysis of genomics and transcriptomics data, assembly of microbial genomes using the distributed PacBio SmrtPortal tool suite, annotation of assembled genomes, and visualisation of the annotated genomes and differential gene expression analyses. This managed Microbial GVL is available at http://abrpi.genome.edu.au
| Function | Incorporated/Connected | |
|---|---|---|
| Genomics | Assembly, Mapping | SPAdes, HGAP3 (SMRT), BWA-MEM, Bowtie2 |
| Variant Calling | Snippy | |
| Genome Annotation | Prokka, WebApollo | |
| Transcriptomics | Read Counts, Gene Expression | Htseq-count, DESeq2, Voom, DeGust |
| Proteomics | Protein Identification | X!tandem, Limma |
| Metabolomics | Metabolite Identification | XCMS, R package (MA) |
| Metabolic Pathway Analysis | MetaCyc/BioCyc, Pathway Tools | |
| Visualisation | Phylogenetics Trees | FastTree |
| Genome Browsers | IGV, JBrowse | |
| Metabolic Pathway Visualisation | Pathway Tools | |
| Multi-Omics Integrative Analysis | Overlay of multi-omics data on metabolic pathways | MetaCyc/BioCyc, Pathway Tools |